rs13355682

Positions:

• chr5-180364487-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.179 in 152,124 control chromosomes in the GnomAD database, including 2,643 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.18 (2643 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.887

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27128 AN: 152006 Hom.: 2634 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.152

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.174

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.179 AC: 27166 AN: 152124 Hom.: 2643 Cov.: 32 AF XY: 0.181 AC XY: 13460 AN XY: 74360

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.183

Alfa AF: 0.159 Hom.: 400

Bravo AF: 0.176

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs13355682; hg19: chr5-179791487;